From 9092ed0f2e00fc4dee6f21c73717e73a46123393 Mon Sep 17 00:00:00 2001
From: Jairo H Migueles <jairo.hidalgo.migueles@gmail.com>
Date: Thu, 5 Oct 2023 07:51:52 +0200
Subject: [PATCH 01/14] sleep onset to onset window implemented in part 5 and
 documentation expanded

---
 R/g.part5.R            | 12 ++++++++++--
 R/g.part5.definedays.R | 19 +++++++++++++++++++
 R/g.report.part5.R     |  8 ++++----
 man/GGIR.Rd            |  2 +-
 vignettes/GGIR.Rmd     |  6 +++---
 5 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/R/g.part5.R b/R/g.part5.R
index bd5fc401b..750a300d1 100644
--- a/R/g.part5.R
+++ b/R/g.part5.R
@@ -410,6 +410,7 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                   #-------------------------------
                   # ignore all nights in 'inights' before the first waking up and after the last waking up
                   FM = which(diff(ts$diur) == -1)
+                  SO = which(diff(ts$diur) == 1)
                   # now 0.5+6+0.5 midnights and 7 days
                   for (timewindowi in params_output[["timewindow"]]) {
                     nightsi = nightsi_bu
@@ -419,6 +420,11 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                         # ignore first and last midnight because we did not do sleep detection on it
                         nightsi = nightsi[nightsi > FM[1] & nightsi < FM[length(FM)]]
                       }
+                    } else if (timewindowi == "OO") {
+                      if (length(SO) > 0) {
+                        # ignore data before the first sleep onset and after the last sleep onset
+                        nightsi = nightsi[nightsi > SO[1] & nightsi < SO[length(SO)]]
+                      }
                     } else {
                       # if first night is missing then nights needs to align with diur
                       startend_sleep = which(abs(diff(ts$diur)) == 1)
@@ -428,8 +434,10 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                     }
                     if (timewindowi == "MM") {
                       Nwindows = length(nightsi) + 1
-                    } else {
+                    } else if (timewindowi == "WW") {
                       Nwindows = length(which(diff(ts$diur) == -1))
+                    } else if (timewindowi == "OO") {
+                      Nwindows = length(which(diff(ts$diur) == 1))
                     }
                     indjump = 1
                     qqq_backup = c()
@@ -442,11 +450,11 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                     }
                     for (wi in 1:Nwindows) { #loop through 7 windows (+1 to include the data after last awakening)
                       # Define indices of start and end of the day window (e.g. midnight-midnight, or waking-up or wakingup
-                      
                       defdays = g.part5.definedays(nightsi, wi, indjump,
                                                    nightsi_bu, epochSize = ws3new, qqq_backup, ts, 
                                                    timewindowi, Nwindows, qwindow = params_247[["qwindow"]],
                                                    ID = ID)
+                      print(ts[defdays$qqq, 1:2])
                       qqq = defdays$qqq
                       qqq_backup = defdays$qqq_backup
                       segments = defdays$segments
diff --git a/R/g.part5.definedays.R b/R/g.part5.definedays.R
index d968b99c3..6e83bd90a 100644
--- a/R/g.part5.definedays.R
+++ b/R/g.part5.definedays.R
@@ -156,6 +156,25 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
       names(segments) = paste(start, end, sep = "-")
       segments_names = "WW"
     }
+  } else if (timewindowi == "OO") {
+    if (wi <= (Nwindows - 1)) { # all full wake to wake days
+      qqq[1] = which(diff(ts$diur) == 1)[wi] + 1
+      qqq[2] = which(diff(ts$diur) == 1)[wi + 1]
+    } else {
+      # time after last reliable waking up (this can be more than 24 hours)
+      # ignore this day, because if the night was ignored for sleep analysis
+      # then the description of the day in part 5 including that night is
+      # not informative.
+      qqq = c(NA, NA)
+    }
+    # build up segments
+    if (!is.na(qqq[1]) & !is.na(qqq[2])) {
+      segments = list(qqq)
+      start = substr(ts$time[qqq[1]], 12, 19)
+      end = substr(ts$time[qqq[2]], 12, 19)
+      names(segments) = paste(start, end, sep = "-")
+      segments_names = "OO"
+    }
   }
   return(invisible(list(qqq = qqq, qqq_backup = qqq_backup, 
                         segments = segments, segments_names = segments_names)))
diff --git a/R/g.report.part5.R b/R/g.report.part5.R
index c93c8b60e..24b3ac19c 100644
--- a/R/g.report.part5.R
+++ b/R/g.report.part5.R
@@ -45,7 +45,7 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
       }
       # Note: Below we intentionally only sets a criteria on daytime, because for
       # the night time we only need start and end of the SPT window.
-      if (window == "WW") {
+      if (window == "WW" | window == "OO") {
         indices = which(x$nonwear_perc_day <= maxpernwday &
                           x$dur_spt_min > 0 & x$dur_day_min > 0 & include_window == TRUE)
       } else if (window == "MM") {
@@ -153,8 +153,8 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
     # split results to different spreadsheets in order to minimize individual
     # filesize and to ease organising dataset
     uwi = as.character(unique(outputfinal$window))
-    if (!all(uwi %in% c("MM", "WW"))) {
-      uwi = c(uwi[uwi %in% c("MM", "WW")], "Segments")
+    if (!all(uwi %in% c("MM", "WW", "OO"))) {
+      uwi = c(uwi[uwi %in% c("MM", "WW", "OO")], "Segments")
     }
     uTRLi = as.character(unique(outputfinal$TRLi))
     uTRMi = as.character(unique(outputfinal$TRMi))
@@ -197,7 +197,7 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
                            "-", uTRVi[h3], "-", usleepparam[h4]))
               }
               select_window = as.character(outputfinal$window) == uwi[j]
-              if (!(uwi[j] %in% c("MM", "WW"))) select_window = !(as.character(outputfinal$window) %in% c("MM", "WW"))
+              if (!(uwi[j] %in% c("MM", "WW", "OO"))) select_window = !(as.character(outputfinal$window) %in% c("MM", "WW", "OO"))
               seluwi = which(select_window &
                                as.character(outputfinal$TRLi) == uTRLi[h1] &
                                as.character(outputfinal$TRMi) == uTRMi[h2] &
diff --git a/man/GGIR.Rd b/man/GGIR.Rd
index 9c7107c0d..f3eb14dfd 100755
--- a/man/GGIR.Rd
+++ b/man/GGIR.Rd
@@ -1269,7 +1269,7 @@ GGIR(mode = 1:5,
         Character (default = c("MM", "WW")).
         In \link{g.part5}: Timewindow over which summary statistics are derived.
         Value can be "MM" (midnight to midnight), "WW" (waking time to waking time),
-        or both c("MM","WW").}
+        "OO" (sleep onset to sleep onset), or any combination of them.}
 
       \item{save_ms5rawlevels}{
         Boolean (default = FALSE).
diff --git a/vignettes/GGIR.Rmd b/vignettes/GGIR.Rmd
index d566862a3..c8587253d 100644
--- a/vignettes/GGIR.Rmd
+++ b/vignettes/GGIR.Rmd
@@ -482,8 +482,8 @@ For an explanation on how time use analysis is performed see section
         Here, the full 25 minutes would count towards the duration of
         the MVPA bout.
 -   `timewindow` to specify whether days should be defined from midnight
-    to midnight `"MM"`, from waking-up to waking-up `"WW"`, or both
-    `c("MM","WW")`.
+    to midnight `"MM"`, from waking-up to waking-up `"WW"`, from sleep onset
+    to sleep onset `"OO"`, or any combination of them.
 -   Configure durations of bouts: `boutdur.mvpa`, `boutdur.in`, and
     `boutdur.lig`. Note that this can be a vector of multiple values
     indicating the minimum and maximum duration of subsequent bout
@@ -1612,7 +1612,7 @@ correspond to the date of analysis.
 | SleepPeriodTime      | Is 1 if SPT is detected, 0 if not. Note that this refers to the combined usage of guider and detected sustained inactivity bouts (rest periods).|
 | invalidepoch         | Is 1 if epoch was detect as invalid (e.g. non-wear), 0 if not.       |
 | guider   | Is 1 if guider method detect epoch as SPT (e.g. sleeplog, HDCZA), 0 if not. You will not find here which guider is used, for this see other GGIR output.    |
-| window   | Numeric indicator of the analysis window in the recording. If timewindow = "MM" then these correspond to calendar days, if timewindow = "WW" then these correspond to which wakingup-wakingup window in the recording. So, in a recording of one week you may find window numbers 1, 2, 3, 4, 5 and 6.|
+| window   | Numeric indicator of the analysis window in the recording. If timewindow = "MM" then these correspond to calendar days, if timewindow = "WW" then these correspond to which wakingup-wakingup window in the recording, if timewindow = "OO" then these correspond to which sleeponset-sleeponset window in the recording. So, in a recording of one week you may find window numbers 1, 2, 3, 4, 5 and 6.|
 | class_id | The behavioural class codes are documented in the exported csv file meta/ms5outraw/behaviouralcodes.csv. Class codes above class 8 will be analysis specific, because it depends on the number time variants of the bouts used. For example, if you look at MVPA lasting 1-10, 10-20, 30-40 then all of them will have their own class_id. |
 | invalid_fullwindow   | Fraction of the window (see above) that represents invalid data. I added this to make it easier to filter the timeseries based on whether days are valid or not.         |
 | invalid_sleepperiod  | Fraction of SPT within the current window that represents invalid data.          |

From 8c71177303ea7f8ae246125cafd2d986fb52023a Mon Sep 17 00:00:00 2001
From: Jairo H Migueles <jairo.hidalgo.migueles@gmail.com>
Date: Thu, 5 Oct 2023 07:54:42 +0200
Subject: [PATCH 02/14] update NEWS

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index c57b52edd..6d5eee42e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -10,6 +10,8 @@
 
 - Fix recently introduced bug where GGIR environment was not exported to cluster in GGIR part 1, 2, 3, and 5 #910
 
+- Part 5: Implemented sleep onset to sleep onset timewindow ("OO") #931
+
 # CHANGES IN GGIR VERSION 2.10-3
 
 - Part 1: Fixed minor bug in ismovisens that failed when datadir started with "./" #897

From 01823d56ff23c316b8907ed60f1d0229de3a2423 Mon Sep 17 00:00:00 2001
From: Jairo H Migueles <jairo.hidalgo.migueles@gmail.com>
Date: Thu, 5 Oct 2023 08:16:07 +0200
Subject: [PATCH 03/14] remove line introduced for debugging purposes

---
 R/g.part5.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/g.part5.R b/R/g.part5.R
index 750a300d1..89b45113a 100644
--- a/R/g.part5.R
+++ b/R/g.part5.R
@@ -454,7 +454,6 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                                                    nightsi_bu, epochSize = ws3new, qqq_backup, ts, 
                                                    timewindowi, Nwindows, qwindow = params_247[["qwindow"]],
                                                    ID = ID)
-                      print(ts[defdays$qqq, 1:2])
                       qqq = defdays$qqq
                       qqq_backup = defdays$qqq_backup
                       segments = defdays$segments

From 99bfc46bd19c6eac5bf1fa6560f686b9acef08da Mon Sep 17 00:00:00 2001
From: Jairo H Migueles <jairo.hidalgo.migueles@gmail.com>
Date: Thu, 5 Oct 2023 10:52:34 +0200
Subject: [PATCH 04/14] test for timewindow = c(MM, WW, OO)

---
 tests/testthat/test_chainof5parts.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test_chainof5parts.R b/tests/testthat/test_chainof5parts.R
index b6247a089..ad4f39507 100644
--- a/tests/testthat/test_chainof5parts.R
+++ b/tests/testthat/test_chainof5parts.R
@@ -148,7 +148,7 @@ test_that("chainof5parts", {
           overwrite = TRUE, excludefirstlast = FALSE, do.parallel = do.parallel,
           frag.metrics = "all", save_ms5rawlevels = TRUE,
           part5_agg2_60seconds = TRUE, do.sibreport = TRUE, nap_model = "hip3yr",
-          iglevels = 1)
+          iglevels = 1, timewindow = c("MM", "WW", "OO"))
   sibreport_dirname = "output_test/meta/ms5.outraw/sib.reports"
   expect_true(dir.exists(sibreport_dirname))
   expect_true(file.exists(paste0(sibreport_dirname, "/sib_report_123A_testaccfile_T5A5.csv")))
@@ -161,9 +161,11 @@ test_that("chainof5parts", {
   
   expect_true(dir.exists(dirname))
   expect_true(file.exists(rn[1]))
-  expect_that(nrow(output),equals(4))
+  expect_that(nrow(output),equals(5)) # changed because OO window is exported
   expect_that(ncol(output),equals(197))
   expect_that(round(as.numeric(output$wakeup[2]), digits = 4), equals(36))
+  expect_that(as.numeric(output$dur_day_spt_min[4]), equals(1150)) # WW window duration
+  expect_that(as.numeric(output$dur_day_spt_min[5]), equals(1680)) # OO window duration
   dirname_raw = "output_test/meta/ms5.outraw/40_100_400"
   rn2 = dir(dirname_raw,full.names = TRUE, recursive = T)
   expect_true(file.exists(rn2[1]))
@@ -187,6 +189,9 @@ test_that("chainof5parts", {
   expect_true(file.exists("output_test/results/part4_nightsummary_sleep_cleaned.csv"))
   expect_true(file.exists("output_test/results/part4_summary_sleep_cleaned.csv"))
   expect_true(file.exists("output_test/results/file summary reports/Report_123A_testaccfile.csv.pdf"))
+  expect_true(file.exists("output_test/results/part5_daysummary_MM_L40M100V400_T5A5.csv"))
+  expect_true(file.exists("output_test/results/part5_daysummary_WW_L40M100V400_T5A5.csv"))
+  expect_true(file.exists("output_test/results/part5_daysummary_OO_L40M100V400_T5A5.csv"))
   dn = "output_test"
   
   #=======================

From 968723033a966049229d3d493571c25be437ce46 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 11:56:49 +0200
Subject: [PATCH 05/14] do not delete start_end_window column

---
 R/g.report.part5.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/g.report.part5.R b/R/g.report.part5.R
index 215623030..cf3c31d8e 100644
--- a/R/g.report.part5.R
+++ b/R/g.report.part5.R
@@ -210,7 +210,7 @@ g.report.part5 = function(metadatadir = c(), f0 = c(), f1 = c(), loglocation = c
                 CN = colnames(outputfinal)
                 outputfinal2 = outputfinal
                 colnames(outputfinal2) = CN
-                delcol = grep(pattern = "window|TRLi|TRMi|TRVi|sleepparam",
+                delcol = grep(pattern = "TRLi|TRMi|TRVi|sleepparam",
                               x = colnames(outputfinal2))
                 if (uwi[j] != "Segments") {
                   delcol = c(delcol, which(colnames(outputfinal2) == "window"))

From 70b5bd754cf6137a81b0f38e5ff4a1a2f2059246 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 11:59:12 +0200
Subject: [PATCH 06/14] fix redundancy + do not extract time by assuming
 character positions this does not work with midnight

---
 R/g.part5.definedays.R | 42 +++++++++++++-----------------------------
 1 file changed, 13 insertions(+), 29 deletions(-)

diff --git a/R/g.part5.definedays.R b/R/g.part5.definedays.R
index 6e83bd90a..a4d6de27a 100644
--- a/R/g.part5.definedays.R
+++ b/R/g.part5.definedays.R
@@ -87,7 +87,7 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
     # in MM, also define segments of the day based on qwindow
     if (!is.na(qqq[1]) & !is.na(qqq[2])) {
       fullQqq = qqq[1]:qqq[2]
-      lastepoch = substr(ts$time[qqq[2]], 12, 19)
+      lastepoch = format(ts$time[qqq[2]],  "%H:%M:%S")
       qnames = NULL
       if (is.data.frame(qwindow)) {
         date_of_interest = substr(ts$time[qqq[1]], 1, 10)
@@ -137,13 +137,14 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
       }
       names(segments) = segments_timing
     }
-  } else if (timewindowi == "WW") {
-    if (wi <= (Nwindows - 1)) { # all full wake to wake days
-      qqq[1] = which(diff(ts$diur) == -1)[wi] + 1
-      qqq[2] = which(diff(ts$diur) == -1)[wi + 1]
+  } else if (timewindowi == "WW" || timewindowi == "OO") {
+    windowEdge = ifelse(timewindowi == "WW", yes = -1, no = 1)
+    if (wi <= (Nwindows - 1)) { # all full windows
+      qqq[1] = which(diff(ts$diur) == windowEdge)[wi] + 1
+      qqq[2] = which(diff(ts$diur) == windowEdge)[wi + 1]
     } else {
-      # time after last reliable waking up (this can be more than 24 hours)
-      # ignore this day, because if the night was ignored for sleep analysis
+      # time after last reliable waking up or onset (this can be more than 24 hours)
+      # ignore this window, because if the night was ignored for sleep analysis
       # then the description of the day in part 5 including that night is
       # not informative.
       qqq = c(NA, NA)
@@ -151,30 +152,13 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
     # build up segments
     if (!is.na(qqq[1]) & !is.na(qqq[2])) {
       segments = list(qqq)
-      start = substr(ts$time[qqq[1]], 12, 19)
-      end = substr(ts$time[qqq[2]], 12, 19)
+      start = format(ts$time[qqq[1]], "%H:%M:%S")
+      end = format(ts$time[qqq[2]], "%H:%M:%S")
+      if (timewindowi == "OO") browser()
       names(segments) = paste(start, end, sep = "-")
-      segments_names = "WW"
-    }
-  } else if (timewindowi == "OO") {
-    if (wi <= (Nwindows - 1)) { # all full wake to wake days
-      qqq[1] = which(diff(ts$diur) == 1)[wi] + 1
-      qqq[2] = which(diff(ts$diur) == 1)[wi + 1]
-    } else {
-      # time after last reliable waking up (this can be more than 24 hours)
-      # ignore this day, because if the night was ignored for sleep analysis
-      # then the description of the day in part 5 including that night is
-      # not informative.
-      qqq = c(NA, NA)
-    }
-    # build up segments
-    if (!is.na(qqq[1]) & !is.na(qqq[2])) {
-      segments = list(qqq)
-      start = substr(ts$time[qqq[1]], 12, 19)
-      end = substr(ts$time[qqq[2]], 12, 19)
-      names(segments) = paste(start, end, sep = "-")
-      segments_names = "OO"
+      segments_names = timewindowi
     }
+    
   }
   return(invisible(list(qqq = qqq, qqq_backup = qqq_backup, 
                         segments = segments, segments_names = segments_names)))

From ed843d8a8c8d889bdd946bcef9d5f86d9ffeffd4 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 12:01:11 +0200
Subject: [PATCH 07/14] Account for OO scenario in g.part5_onsetwaketiming

---
 R/g.part5.onsetwaketiming.R | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/g.part5.onsetwaketiming.R b/R/g.part5.onsetwaketiming.R
index 1bdf1e926..333cd722f 100644
--- a/R/g.part5.onsetwaketiming.R
+++ b/R/g.part5.onsetwaketiming.R
@@ -2,22 +2,23 @@ g.part5.onsetwaketiming = function(qqq, ts, min, sec, hour, timewindowi) {
   onset = wake = 0
   skiponset = TRUE; skipwake = TRUE
   # Onset index
-  if (timewindowi == "WW") {
-    onseti = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2]-1)]) == 1)+1]
-    if (length(onseti) > 1) {
-      onseti = onseti[length(onseti)] # in the case if MM use last onset
-    }
+  if (timewindowi == "OO") {
+    # For OO onset is by definition the start and end of the window
+    onseti = qqq[2] + 1
   } else {
-    onseti = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2]-1)]) == 1)+1]
+    # For WW and MM onset needs to be search in the window
+    onseti = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2] - 1)]) == 1) + 1]
     if (length(onseti) > 1) {
       onseti = onseti[length(onseti)] # in the case if MM use last onset
     }
   }
   # Wake index
   if (timewindowi == "WW") {
-    wakei = qqq[2]+1
+    # For WW wake is by definition the start and end of the window
+    wakei = qqq[2] + 1
   } else {
-    wakei = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2]-1)]) == -1)+1]
+    # For OO and MM wake needs to be search in the window
+    wakei = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2] - 1)]) == -1) + 1]
     if (length(wakei) > 1) wakei = wakei[1] # in the case if MM use first wake-up time
   }
   # Onset time

From d9ffefaf627fd580232f83e5cd1172d78430e7be Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 12:01:56 +0200
Subject: [PATCH 08/14] account for OO in g.part5_analyseSegment

---
 R/g.part5_analyseSegment.R | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/R/g.part5_analyseSegment.R b/R/g.part5_analyseSegment.R
index 69685c8b7..adf386a6a 100644
--- a/R/g.part5_analyseSegment.R
+++ b/R/g.part5_analyseSegment.R
@@ -49,7 +49,7 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
   # This code extract them the time series (ts) object create in g.part5
   # Note that this means that for MM windows there can be multiple or no wake or onsets
   date = as.Date(ts$time[segStart + 1])
-  if (add_one_day_to_next_date == TRUE & timewindowi == "WW") { # see below for explanation
+  if (add_one_day_to_next_date == TRUE & timewindowi %in% c("WW", "OO")) { # see below for explanation
     date = date + 1
     add_one_day_to_next_date = FALSE
   }
@@ -73,6 +73,12 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
     # So, for next window we have to do date = date + 1
     add_one_day_to_next_date = TRUE
   }
+  if (onset < 24 & timewindowi == "OO") {
+    # onset before midnight means that next OO window
+    # will start a day before the day we refer to when discussing it's SPT
+    # So, for next window we have to do date = date + 1
+    add_one_day_to_next_date = TRUE
+  }
   # Add to dsummary output matrix
   if (skiponset == FALSE) {
     dsummary[si,fi] = onset
@@ -440,7 +446,7 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
         }
       }
       fi = fi + Nluxt
-      if (timewindowi == "WW") {
+      if (timewindowi %in% c("WW", "OO")) {
         # LUX per segment of the day
         luxperseg = g.part5.lux_persegment(ts, sse,
                                            LUX_day_segments = params_247[["LUX_day_segments"]],
@@ -487,7 +493,6 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
                   columnIndex = fi)
   timeList = list(ts = ts,
                   epochSize = ws3new)
-  
   invisible(list(
     indexlog = indexlog,
     ds_names = ds_names,

From 607cee96055dee0129796ade81e8c03bc6123c04 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 13:49:05 +0200
Subject: [PATCH 09/14] move time stamp conversion outside agg2_60seconds block
 to standardise time format regardless of aggregation

---
 R/g.part5.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/g.part5.R b/R/g.part5.R
index 89b45113a..4f77f6484 100644
--- a/R/g.part5.R
+++ b/R/g.part5.R
@@ -276,8 +276,10 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
             # Add first waking up time, if it is missing:
             ts = g.part5.addfirstwake(ts, summarysleep = summarysleep_tmp2, nightsi, sleeplog, ID,
                                       Nepochsinhour, SPTE_end)
+            # Convert time column regardless of whether it is aggregated to secure standard time format
+            ts$time = iso8601chartime2POSIX(ts$time,tz = params_general[["desiredtz"]])
             if (params_general[["part5_agg2_60seconds"]] == TRUE) { # Optionally aggregate to 1 minute epoch:
-              ts$time_num = floor(as.numeric(iso8601chartime2POSIX(ts$time,tz = params_general[["desiredtz"]])) / 60) * 60
+              ts$time_num = floor(as.numeric(ts$time) / 60) * 60
               
               # only include angle if angle is present
               angleColName = ifelse("angle" %in% names(ts), yes = "angle", no = NULL)

From bc26dd05dd49105c392342045e16314874054bd5 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 13:51:37 +0200
Subject: [PATCH 10/14] handle missing sleep for first and last night because
 ignored in part 4, ensure OO window has correct date and timeings, fix onset
 index

---
 R/g.part5.addfirstwake.R    |  8 ++++----
 R/g.part5.definedays.R      |  8 +++-----
 R/g.part5.onsetwaketiming.R |  4 ++--
 R/g.part5_analyseSegment.R  | 22 +++++++++++++---------
 4 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/R/g.part5.addfirstwake.R b/R/g.part5.addfirstwake.R
index 1fd0337f5..ac292813c 100644
--- a/R/g.part5.addfirstwake.R
+++ b/R/g.part5.addfirstwake.R
@@ -1,4 +1,4 @@
-g.part5.addfirstwake =function(ts, summarysleep, nightsi, sleeplog, ID, 
+g.part5.addfirstwake = function(ts, summarysleep, nightsi, sleeplog, ID, 
                                Nepochsinhour, SPTE_end) {
   # Note related to if first and last night were ignored in part 4:
   # - diur lacks the first and last night at this point in the code.
@@ -72,7 +72,7 @@ g.part5.addfirstwake =function(ts, summarysleep, nightsi, sleeplog, ID,
     }
     if (is.na(wake_night1_index)) wake_night1_index = 0
     if (wake_night1_index < firstwake & wake_night1_index > 1 & (wake_night1_index-1) > nightsi[1]) {
-      ts$diur[nightsi[1]:(wake_night1_index-1)] = 1
+      ts$diur[1:(wake_night1_index-1)] = 1
     } else {
       # Person slept only during the afternoon on day 2
       # And there is no sleep data available for the first night
@@ -82,8 +82,8 @@ g.part5.addfirstwake =function(ts, summarysleep, nightsi, sleeplog, ID,
       # and merging of the sleep variables is still consistent with
       # the other recording.
       dummywake = max(firstonset - round(Nepochsinhour/12), nightsi[1] + round(Nepochsinhour * 6))
-      ts$diur[nightsi[1]:dummywake] = 1 
-      ts$nonwear[nightsi[1]:firstonset] = 1
+      ts$diur[1:dummywake] = 1 
+      ts$nonwear[1:firstonset] = 1
     }
   }
   return(ts)
diff --git a/R/g.part5.definedays.R b/R/g.part5.definedays.R
index a4d6de27a..576c92855 100644
--- a/R/g.part5.definedays.R
+++ b/R/g.part5.definedays.R
@@ -74,14 +74,13 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
         }
       }
     } else {
+      qqq = c(NA, NA)
       if (length(qqq_backup) > 1) {
         # if there is remaining time after previous day...
-        if (Nts > qqq_backup[2]) {
+        # and if this is less than 24 hours (necessary if sleep is ignored for last night
+        if (Nts - qqq_backup[2] < 24 * (60 / epochSize) * 60) {
           qqq = c(qqq_backup[2] + 1, Nts)
         }
-      } else {
-        # else, do not analyse this day
-        qqq = c(NA, NA)
       }
     }
     # in MM, also define segments of the day based on qwindow
@@ -154,7 +153,6 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
       segments = list(qqq)
       start = format(ts$time[qqq[1]], "%H:%M:%S")
       end = format(ts$time[qqq[2]], "%H:%M:%S")
-      if (timewindowi == "OO") browser()
       names(segments) = paste(start, end, sep = "-")
       segments_names = timewindowi
     }
diff --git a/R/g.part5.onsetwaketiming.R b/R/g.part5.onsetwaketiming.R
index 333cd722f..aa3fbce6e 100644
--- a/R/g.part5.onsetwaketiming.R
+++ b/R/g.part5.onsetwaketiming.R
@@ -4,10 +4,10 @@ g.part5.onsetwaketiming = function(qqq, ts, min, sec, hour, timewindowi) {
   # Onset index
   if (timewindowi == "OO") {
     # For OO onset is by definition the start and end of the window
-    onseti = qqq[2] + 1
+    onseti = qqq[1] + 1
   } else {
     # For WW and MM onset needs to be search in the window
-    onseti = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2] - 1)]) == 1) + 1]
+    onseti = c(qqq[1]:qqq[2])[which(diff(ts$diur[qqq[1]:(qqq[2] - 1)]) == 1)] + 1
     if (length(onseti) > 1) {
       onseti = onseti[length(onseti)] # in the case if MM use last onset
     }
diff --git a/R/g.part5_analyseSegment.R b/R/g.part5_analyseSegment.R
index adf386a6a..a34b99b00 100644
--- a/R/g.part5_analyseSegment.R
+++ b/R/g.part5_analyseSegment.R
@@ -48,7 +48,7 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
   # The following is to avoid issue with merging sleep variables from part 4
   # This code extract them the time series (ts) object create in g.part5
   # Note that this means that for MM windows there can be multiple or no wake or onsets
-  date = as.Date(ts$time[segStart + 1])
+  date = as.Date(ts$time[segStart + 1], tz = params_general[["desiredtz"]])
   if (add_one_day_to_next_date == TRUE & timewindowi %in% c("WW", "OO")) { # see below for explanation
     date = date + 1
     add_one_day_to_next_date = FALSE
@@ -73,9 +73,9 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
     # So, for next window we have to do date = date + 1
     add_one_day_to_next_date = TRUE
   }
-  if (onset < 24 & timewindowi == "OO") {
-    # onset before midnight means that next OO window
-    # will start a day before the day we refer to when discussing it's SPT
+  if (onset > 24 & timewindowi == "OO") {
+    # onset after midnight means that next OO window
+    # will start a day after the day we refer to when discussing it's SPT
     # So, for next window we have to do date = date + 1
     add_one_day_to_next_date = TRUE
   }
@@ -427,11 +427,15 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
     # LIGHT, IF AVAILABLE
     if ("lightpeak" %in% colnames(ts) & length(params_247[["LUX_day_segments"]]) > 0) {
       # mean LUX
-      dsummary[si,fi] =  round(max(ts$lightpeak[sse[ts$diur[sse] == 0]], na.rm = TRUE), digits = 1)
-      dsummary[si,fi + 1] = round(mean(ts$lightpeak[sse[ts$diur[sse] == 0]], na.rm = TRUE), digits = 1)
-      dsummary[si,fi + 2] = round(mean(ts$lightpeak[sse[ts$diur[sse] == 1]], na.rm = TRUE), digits = 1)
-      dsummary[si,fi + 3] = round(mean(ts$lightpeak[sse[ts$diur[sse] == 0 & ts$ACC[sse] > TRMi]], na.rm = TRUE),
-                                  digits = 1)
+      if (length(which(ts$diur[sse] == 0)) > 0 & length(which(ts$diur[sse] == 1)) > 0) {
+        dsummary[si,fi] =  round(max(ts$lightpeak[sse[ts$diur[sse] == 0]], na.rm = TRUE), digits = 1)
+        dsummary[si,fi + 1] = round(mean(ts$lightpeak[sse[ts$diur[sse] == 0]], na.rm = TRUE), digits = 1)
+        dsummary[si,fi + 2] = round(mean(ts$lightpeak[sse[ts$diur[sse] == 1]], na.rm = TRUE), digits = 1)
+        dsummary[si,fi + 3] = round(mean(ts$lightpeak[sse[ts$diur[sse] == 0 & ts$ACC[sse] > TRMi]], na.rm = TRUE),
+                                    digits = 1)
+      } else {
+        dsummary[si,fi:(fi + 3)] = NA
+      }
       ds_names[fi:(fi + 3)] = c("LUX_max_day", "LUX_mean_day", "LUX_mean_spt", "LUX_mean_day_mvpa"); fi = fi + 4
       # time in LUX ranges
       Nluxt = length(params_247[["LUXthresholds"]])

From 4fba2354db299b98f8f2fb6e2b32c729f2b365f6 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 13:56:19 +0200
Subject: [PATCH 11/14] rephrase code comment

---
 R/g.part5.definedays.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/g.part5.definedays.R b/R/g.part5.definedays.R
index 576c92855..e500bd4a3 100644
--- a/R/g.part5.definedays.R
+++ b/R/g.part5.definedays.R
@@ -77,7 +77,9 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
       qqq = c(NA, NA)
       if (length(qqq_backup) > 1) {
         # if there is remaining time after previous day...
-        # and if this is less than 24 hours (necessary if sleep is ignored for last night
+        # but only do this if there is less than 24 hours
+        # this is necessary if sleep is ignored for last night as
+        # that would include the entire last day
         if (Nts - qqq_backup[2] < 24 * (60 / epochSize) * 60) {
           qqq = c(qqq_backup[2] + 1, Nts)
         }

From 499c175e0238ca84dbc0f22f6a96783a7352bbca Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 14:07:22 +0200
Subject: [PATCH 12/14] remove conversion to iso8601 from unit-test because
 g.part5.definedays no longer expects this

---
 tests/testthat/test_part5_qwindow.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/testthat/test_part5_qwindow.R b/tests/testthat/test_part5_qwindow.R
index e82ae80cb..ebc6f8ebf 100644
--- a/tests/testthat/test_part5_qwindow.R
+++ b/tests/testthat/test_part5_qwindow.R
@@ -6,10 +6,9 @@ test_that("g.part5.definedays considers qwindow to generate segments", {
   # set windows
   timestamp = seq.POSIXt(from = as.POSIXct("2022-01-01 00:00:00"), 
                          to = as.POSIXct("2022-01-04 23:59:00"), by = 60)
-  timestamp = POSIXtime2iso8601(timestamp, tz = "")
   ts = data.frame(timestamp = timestamp,
                   ACC = 0)
-  nightsi = grep("00:00:00", ts$timestamp)
+  nightsi = grep("00:00:00", format(ts$timestamp))
   qwindow = c(7, 18)
   
   definedays = g.part5.definedays(nightsi = nightsi, wi = 1, indjump = 1, 

From 63646e016e5ee3a08d7f4e4b3e9289dc6a978939 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 11 Oct 2023 14:29:32 +0200
Subject: [PATCH 13/14] minor edits to code comments

---
 R/g.part5.R                | 3 ++-
 R/g.part5.definedays.R     | 9 +++++----
 R/g.part5_analyseSegment.R | 4 ++--
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/g.part5.R b/R/g.part5.R
index 4f77f6484..59229cdde 100644
--- a/R/g.part5.R
+++ b/R/g.part5.R
@@ -276,7 +276,8 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
             # Add first waking up time, if it is missing:
             ts = g.part5.addfirstwake(ts, summarysleep = summarysleep_tmp2, nightsi, sleeplog, ID,
                                       Nepochsinhour, SPTE_end)
-            # Convert time column regardless of whether it is aggregated to secure standard time format
+            # Convert time column from iso8601 to POSIX regardless of whether it is aggregated
+            # to ensure the format is consistent
             ts$time = iso8601chartime2POSIX(ts$time,tz = params_general[["desiredtz"]])
             if (params_general[["part5_agg2_60seconds"]] == TRUE) { # Optionally aggregate to 1 minute epoch:
               ts$time_num = floor(as.numeric(ts$time) / 60) * 60
diff --git a/R/g.part5.definedays.R b/R/g.part5.definedays.R
index e500bd4a3..b1fcce462 100644
--- a/R/g.part5.definedays.R
+++ b/R/g.part5.definedays.R
@@ -76,10 +76,11 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
     } else {
       qqq = c(NA, NA)
       if (length(qqq_backup) > 1) {
-        # if there is remaining time after previous day...
-        # but only do this if there is less than 24 hours
-        # this is necessary if sleep is ignored for last night as
-        # that would include the entire last day
+        # If there is remaining time after previous day...
+        # but only do this if there is less than 24 hours.
+        # This is necessary if sleep is ignored for last night.
+        # In that case the last two calendar days should be ignored
+        # as no sleep onset will be available.
         if (Nts - qqq_backup[2] < 24 * (60 / epochSize) * 60) {
           qqq = c(qqq_backup[2] + 1, Nts)
         }
diff --git a/R/g.part5_analyseSegment.R b/R/g.part5_analyseSegment.R
index a34b99b00..2689e0caf 100644
--- a/R/g.part5_analyseSegment.R
+++ b/R/g.part5_analyseSegment.R
@@ -69,13 +69,13 @@ g.part5_analyseSegment = function(indexlog, timeList, levelList,
   skiponset = onsetwaketiming$skiponset; skipwake = onsetwaketiming$skipwake
   if (wake < 24 & timewindowi == "WW") {
     # waking up before midnight means that next WW window
-    # will start a day before the day we refer to when discussing it's SPT
+    # will start a day before the date we refer to when discussing it's SPT
     # So, for next window we have to do date = date + 1
     add_one_day_to_next_date = TRUE
   }
   if (onset > 24 & timewindowi == "OO") {
     # onset after midnight means that next OO window
-    # will start a day after the day we refer to when discussing it's SPT
+    # will start a date after the date we refer to when discussing it;s SPT
     # So, for next window we have to do date = date + 1
     add_one_day_to_next_date = TRUE
   }

From f0e114689e3b0b1e175f11b442a276009b83e86d Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Thu, 12 Oct 2023 17:10:37 +0200
Subject: [PATCH 14/14] minor rephrasing of changelog

---
 NEWS.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index a59765066..f757aaf21 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,6 +7,9 @@
 - Part 2: Arguments hrs.del.start and hrs.del.end when combined with strategy = 3 and strategy = 5 now count
 relative to start and end of the most active time window as identified.  #905
 
+- Part 5: Added optioned "OO" to argument timewindow, which defines windows from
+sleep Onset to sleep Onset #931
+
 # CHANGES IN GGIR VERSION 2.10-4
 
 - Part 4: Now better able to handle nights without sustained inactivity bouts (rest) #911
@@ -25,8 +28,6 @@ relative to start and end of the most active time window as identified.  #905
 
 - Fix recently introduced bug where GGIR environment was not exported to cluster in GGIR part 1, 2, 3, and 5 #910
 
-- Part 5: Implemented sleep onset to sleep onset timewindow ("OO") #931
-
 # CHANGES IN GGIR VERSION 2.10-3
 
 - Part 1: Fixed minor bug in ismovisens that failed when datadir started with "./" #897